NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1311591 Query DataSets for GSM1311591
Status Public on Jun 01, 2015
Title x050
Sample type RNA
 
Channel 1
Source name Breast tumor tissue
Organism Homo sapiens
Characteristics group: Sporadic
pam50agilent: LumA
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from freshly frozen tumor tissue using Trizol Reagent (Invitrogen) and RNeasy Micro Kit (Qiagen).
Label Cy5
Label protocol RNA was amplified and labeled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer’s protocol.
 
Channel 2
Source name Universal Human Reference RNA (Stratagene)
Organism Homo sapiens
Characteristics reference: Universal Human Reference RNA (Stratagene)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from freshly frozen tumor tissue using Trizol Reagent (Invitrogen) and RNeasy Micro Kit (Qiagen).
Label Cy3
Label protocol RNA was amplified and labeled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer’s protocol.
 
 
Hybridization protocol Fragmentation, hybridization and washing for the spotted arrays were carried out using Agilent Gene Expression Hybridization Kit (Agilent Technologies ) and Gene Expression Wash Buffer Kit (Agilent Technologies) according to the manufacturer’s protocol in a low ozone environment.
Scan protocol Scanned using a Agilent G2565CA Microarray scanner
Description K059
Data processing Scanned images were quantified by Gene Pix Pro 6.0 (Molecular Devices). Bad quality features flagged during feature extraction were removed and the remaining data were pre-processed. Data were background corrected (normexp, offset=50), then within-array normalized by loess normalization method and between-array normalizatized by the quantile method. The normalized values were used to calculate log2 transformed Cy5/Cy3 ratios. Replicate probes were collapsed by calculating the median. The 92 samples were processed together with 154 other breast tumor samples. ComBat method was used for adjustment of the batch effects across the different spotting batches [PMID: 16632515]. In cases of multiple probes per gene symbol only the probe with the maximum mean (Cy5) intensity was kept. Missing expression values were imputed by k-nearest neighbors averaging (k = 10).
 
Submission date Jan 22, 2014
Last update date Jun 01, 2015
Contact name Martin Jakob Larsen
E-mail(s) martin.larsen@rsyd.dk
Organization name Odense University Hospital
Department Dept. of Clinical Genetics
Street address Sdr. Boulevard 29
City Odense C
ZIP/Postal code 5000
Country Denmark
 
Platform ID GPL15932
Series (1)
GSE54275 Microarray gene expression analysis: Batch effect removal improves the cross-platform consistency

Data table header descriptions
ID_REF
VALUE Log2 transformed ratios(Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
CGEN_HUMAN_LIB2_6010321789_0 1.19826185859895
CGEN_HUMAN_LIB2_6010305554_0 -0.278409052999392
CGEN_HUMAN_LIB2_6010316348_0 0.333369385654439
CGEN_HUMAN_LIB2_6010318548_0 0.256276857680677
CGEN_HUMAN_LIB2_6010322653_0 0.346271874351127
CGEN_HUMAN_LIB2_6010306515_0 0.215148955938838
CGEN_HUMAN_LIB2_6010327270_0 -0.67466021746115
CGEN_HUMAN_LIB2_6010305889_0 0.12358992391536
CGEN_HUMAN_LIB2_6010322217_0 0.0517977903050874
CGEN_HUMAN_LIB2_6010300416_0 -1.1160786927425
CGEN_HUMAN_LIB2_6010328195_0 2.90540638393531
CGEN_HUMAN_LIB2_6010311510_0 0.401300565701722
CGEN_HUMAN_LIB2_6010306064_0 -0.607367581476153
CGEN_HUMAN_LIB2_6010325142_0 0.207804285950846
CGEN_HUMAN_LIB2_6010326970_0 1.6754450016887
CGEN_HUMAN_LIB2_6010302501_0 -0.285953025519586
CGEN_HUMAN_LIB2_6010308530_0 -0.605051726668821
CGEN_HUMAN_LIB2_6010328062_0 -0.0642193422964931
CGEN_HUMAN_LIB2_6010328856_0 -0.540147084720959
CGEN_HUMAN_LIB2_6010313980_0 0.210399511836223

Total number of rows: 28919

Table truncated, full table size 1334 Kbytes.




Supplementary file Size Download File type/resource
GSM1311591_x050.gpr.gz 2.7 Mb (ftp)(http) GPR
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap